Effects of geographic isolation on the Bulbophyllum chloroplast genomes

Background Because chloroplast (cp) genome has more conserved structures than nuclear genome and mitochondrial genome, it is a useful tool in estimating the phylogenetic relationships of plants. With a series of researches for cp genomes, there have been comprehensive understandings about the cp genome features. The genus Bulbophyllum widely distributed in Asia, South America, Australia and other places. Therefore, it is an excellent type genus for studying the effects of geographic isolation. Results In this study, the cp genomes of nine Bulbophyllum orchids were newly sequenced and assembled using the next-generation sequencing technology. Based on 19 Asian (AN) and eight South American (SA) Bulbophyllum orchids, the cp genome features of AN clade and SA clade were compared. Comparative analysis showed that there were considerable differences in overall cp genome features between two clades in three aspects, including basic cp genome features, SSC/IRB junctions (JSBs) and mutational hotspots. The phylogenetic analysis and divergence time estimation results showed that the AN clade has diverged from the SA clade in the late Oligocene (21.50–30.12 mya). After estimating the occurrence rates of the insertions and deletions (InDels), we found that the change trends of cp genome structures between two clades were different under geographic isolation. Finally, we compared selective pressures on cp genes and found that long-term geographic isolation made AN and SA Bulbophyllum cp genes evolved variably. Conclusion The results revealed that the overall structural characteristics of Bulbophyllum cp genomes diverged during the long-term geographic isolation, and the crassulacean acid metabolism (CAM) pathway may play an important role in the Bulbophyllum species evolution. Supplementary Information The online version contains supplementary material available at 10.1186/s12870-022-03592-y.


Background
Chloroplasts (cp) are semi-autonomous organelles with their own unique genomes. The cp genomes of terrestrial plants are relatively conservative, with sizes ranging from 120 to 170 kbp, and can be divided into four regions: large single copy (LSC) region, small single copy (SSC) region and two inverted repeat (IR B and IR A ) regions [1,2]. Compared with nuclear genome and mitochondrial genome, cp genome is characterized by conserved structures, which made it a useful tool in estimating the phylogenetic relationships of plants [3,4]. Although the cp gene content and composition are highly conserved, e.g., containing about 120 genes, mainly consisting of three categories: self-replication genes, photosynthesis genes, and RNA genes [5], the cp genomes have undergone structural changes in the long evolutionary process [6], such as IR contraction [7], inversion [8,9], loss of genes and introns [10].

Open Access
*Correspondence: niuzhitaonj@163.com; dingxynj@263.net 1 College of Life Sciences, Nanjing Normal University, Nanjing 210023, China Full list of author information is available at the end of the article In recent years, as the sequencing costs continue to decrease, more and more complete cp genomes were sequenced and assembled, which is helpful for the plant phylogenetic studies. Orchids have become the focus of phylogenetic studies due to rich species, wide distributions and epiphytic habits. Based on 124 orchid cp genomes, Kim et al. (2020) cleared out the relationships of five subfamilies within Orchidaceae (Apostasioideae, Vanilloideae, Cypripedioideae, Orchidoideae and Epidendroideae) [4]. Moreover, there have been comprehensive understandings about the orchid cp genome features. For example, (i) cp genome substitution rates are considerably lower in IR regions than in SC regions [11,12]; (ii) the repeat sequences played an important role in cp genome rearrangements [13][14][15]; (iii) mutational hotspots are genus specific [16]. However, the effects of geographic isolation on the cp genomes have not been investigated.
The genus Bulbophyllum Thou. belongs to the family Orchidaceae Juss., mainly distributed in Asia, South America, Australia and other places [17]. It is one of the largest genera of flowering plants, comprising about 2,000 species, which are predominantly restricted to rainforest habitats [18]. And it is characterized by epiphytic growth, CAM metabolism and fleshy flowers. There are about 105 species in China, which are widely distributed in Guizhou, Guangxi, Yunnan and Fujian provinces [19]. The wide distributions make the genus Bulbophyllum an excellent mode for studying the effects of geographic isolation on the cp genomes. There have been previous studies on the Bulbophyllum phylogenetic relationships. Gamisch et al. (2015) used internal transcribed spacer (ITS) sequences and four short cp genome fragments to study the phylogenetic relationships and estimate divergence times of Madagascar Bulbophyllum [20]. Gamisch et al. (2019) analyzed the evolutionary relationships of Bulbophyllum between different continents with ITS sequences, showing that Asian (AN) clade first separated from other Bulbophyllum orchids, and then South American (SA) clade separated from African Bulbophyllum [18]. Therefore, the Bulbophyllum is an excellent type genus to study the effects of geographical isolation on cp genomes.
In this study, the cp genomes of nine AN Bulbophyllum orchids were newly sequenced and assembled using the next-generation sequencing technology. The comprehensive comparative analyses were performed, based on 27 complete cp genomes of AN and SA Bulbophyllum. The aims of this study were: (1) to uncover the differences in cp genome features between AN clade and SA clade; (2) to assess the effects of long-term geographic isolation on cp genome structures; (3) to investigate the direct causes of the variable selective pressures on cp genes. We believed that this study will give us a comprehensive understanding of the effects of geographic isolation on the complete cp genomes.

Chloroplast genome features
The nine newly sequenced Bulbophyllum cp genomes were circular with the typical quadripartite structure, including a large single copy (LSC), a small single copy (SSC) and a pair of inverted repeats (i.e., IR A and IR B ) (Fig. 1). We combined the published cp genomes of ten AN and eight SA Bulbophyllum orchids with this study's nine AN Bulbophyllum orchids to compare the basic cp genome features of two clades. As shown in Table 1 [17], which indicated that there were significant cp genome differences between two clades. Moreover, the Bulbophyllum cp genomes were well-conserved in gene number and gene order, with 74 protein-coding genes, 30 tRNA genes and 4 rRNA genes.
The levels of the nine newly sequenced cp genome sequence variability were estimated and plotted using mVISTA, with Dendrobium huoshanense as the reference (Fig. S1). As expected, the non-coding regions (intergenic spacers and introns) were more divergent than coding regions, and the SC regions exhibited higher divergence levels than IR regions. Comparative cp genomic analysis of Bulbophyllum revealed a minor organizational variation, which covered an inversion of rpl32.

Repeat and SSR analysis
The Longer dispersed repeats (LDRs) were detected using REPuter and shown in Fig. S2A. The results showed that, (i) the LDRs distribution densities in SSC region were higher than LSC and IR regions (Mann-Whitney two-sided, P < 0.05). (ii) The LDRs in SSC regions were highly varied between two clades (T-test for Independent Samples: P < 0.05). The analysis of simple sequence repeats (SSRs) also revealed the identical trends (Fig.  S2B). Considering the higher LDRs and SSRs distribution densities with the lower GC contents in SSC regions, we conducted correlation tests to see if there were correlative relationships among them. Indeed, significant negative correlations were detected among them (LDRs vs GC contents: Pearson's r = -0.529; SSRs vs GC contents: Pearson's r = -0.977, P < 0.05), which indicated that low GC contents may lead to the SSC regions more variable.

Comparison of sequences flanking IR/SC junctions between Asian and South American clades
The sequences flanking IR/SC junctions in cp genomes were compared. As shown in Fig. 1 and Fig. S3, the Bulbophyllum IR/SC junctions were highly conserved. The SSC/IR A junctions (J SA s) was located in the 5' end of ycf1, which resulted in a pseudogene fragment Ψycf1 (33 to 1,434 bp) in the SSC/IR B junctions (J SB s). Meanwhile, the LSC/IR B junctions (J LB s) were located in rpl22, which leaded Ψrpl22 (10 to 79 bp) in the LSC/IR A junctions (J LA s). Remarkably, IR B expanded progressively from J SB s to ndhF. The main differences between the two clades were in J SB , which can be divided into three types, (A) a relatively long Ψycf1 (796 to 1,434 bp) with a ΨndhF (B.   Meanwhile, there were more type C in SA clade. These results revealed that the evolution of IR/SC junctions between two clades were diversified.

Diverse mutational hotspots between the Asian and South American clades
We extracted a total of 72 intergenic and intronic loci (conserved sites > 100 bp) from two clades and calculated their sequence variabilities (SVs), with D. huoshanense as the reference. As shown in Fig. 2, the SVs in SC regions were significantly higher than IR regions (Mann-Whitney two-sided, P < 0.05). In the AN clade, the top-ten loci (SV = 0.4309 to 0.6177) mainly located in LSC region (eight in LSC and two in SSC) ( Fig. 2A). And in the SA clade, only two mutational hotspots were identical with the AN clade (ccsA-ndhD and clpP-ex1-psbB) (Fig. 2B), which suggested that the evolution of non-coding regions between two clades were disproportional.

Geographic isolation verification
The aligned cp genomes and ITS sequences were connected to test hybridization. The ten AN Bulbophyllum orchids were set as the BAN branch, the seven SA Bulbophyllum orchids were set as the BSO branch, two D. huoshanense species were set as the DHU branch, four D. moniliforme species were set as the DMO branch and five D. officinale species were set as the DOF branch (Fig. S4). The JML results showed that no hybridization occurred between BAN branch and BSO branch. These results proved that there was no gene flow between two clades, which may due to the long periods of geographic isolation.

Phylogenetic analysis and divergence time estimation
The phylogenetic relationships among 27 Bulbophyllum species were reconstructed by 61 angiosperm cp genomes (Table S1). The ML tree exhibited identical topology with the BI tree. As shown in the Fig. 3B, the phylogenetic trees revealed a monophyletic relationship for the orchids with strongly support (bootstrap values = 100/100). Meanwhile, the Bulbophyllum achieved a monophyly with 100/100 bootstrap values, and was sister to Dendrobium. As expected, the 27 Bulbophyllum orchids were divided into the AN clade and SA clade. These results were consistent with previous studies [4,18,25].
ITS sequences and three cp genes (psbA, matK and rbcL) were used to reconstructed the phylogenetic relationships of 27 orchids (including Bulbophyllum, Dendrobium and Phalaenopsis) (Fig. S5). The results supported that 27 Bulbophyllum orchids were strictly divided into two clades. In addition, we found that neither the ITS tree nor the ITS + psbA + matK + rbcL tree was comparable to cp genome tree in bootstrap values. Obviously, the cp genomes have a better performance in studying plant phylogenetic relationships.
The divergence times of 61 orchids were estimated using BEAST2. The topologies of the BEAST tree were almost consistent to ML and BI trees except for B. affine and B. reptans, which may be because reconstructing phylogenetic relationships at the angiosperm-scale hid SNPs that can distinguish between close species (Fig. 3A). In this study, Bulbophyllum was inferred to have diverged from Dendrobium at 36.77 (32.15-41.39) million years ago (mya), and the Bulbophyllum AN clade was inferred to have diverged from SA clade at 25.81 (21.5-30.12) mya. Notably, these results were slightly higher than previous studies [18,25], mainly because cp genome sequences are longer than ITS sequences and other short fragments.

Cp genome structural variation analysis
The insertions and deletions (InDels) were identified in 27 Bulbophyllum cp genomes, with D. huoshanense as outgroup. There were more deletions (5,314 to 14,498 bp) than insertions (4,216 to 10,652 bp) in Bulbophyllum (Fig. 4A). In addition, the distribution of InDels were different between AN and SA clades. For example, (i) the InDels lengths were varied between two clades. The total InDels lengths of AN clade (5,540 to 10,652 bp and 5,314 to 14,498 bp) were higher than SA clade (4,216 to 6,801 bp and 8,466 to 12,642 bp) (Fig. 4A). (ii) Except for partial AN Bulbophyllum species, the InDels distribution densities in SSC region were higher than in LSC and IR regions (Fig. 4B), which indicated that SSC region structure was diversified among two clades. (iii) In addition to InDels distribution densities in different regions, the occurrence rates of InDels between AN and SA clades were also inconsistent (Fig. 4C). The InDels occurrence rates of AN clade (473.01 and 246.90 bp/myr) were higher than SA clade (127.38 and 213.95 bp/myr). These results revealed that the evolution of cp genome structures between two clades were asymmetry.

Evolution analysis of protein-coding genes
The synonymous (dS) and non-synonymous (dN) substitution rates for each protein-coding genes were estimated using codonML, with D. huoshanense as reference. The values of dS (0-0.1973) were higher than dN (0-0.0451) in Bulbophyllum. Although most of ω values between two clades were similar (Fig. 5A), there were some significantly different protein-coding genes, such as atpA, psbZ, rpl16 and atpE (Fig. 5B, Table S2). These genes, which mainly contained photosynthesis and self-replication functions, were mostly distributed  (Table S3). These results indicated that a part of protein-coding genes between two clades were under different selective pressures.
The Branch model of codeML were used to investigate the possible role of positive selection in driving proteincoding gene evolution among three branches (Bulbophyllum branch, AN branch and SA branch). The comparison showed that a part of genes was under different selective pressures. For example, there were six genes (psbB, psbF, rbcL, rpl23, ycf3 and ycf2) were found with positive selection in the Bulbophyllum branch; and five genes (matK, psbJ, ycf2, psbZ and psbF) were found in the AN branch; and three genes (rpl2, rpl36 and ycf2) were found in the SA branch (Fig. 5C). Most of them were in the LSC region (Table S4). The positively selective protein-coding genes between AN and SA branches were different, which suggested that different environments diversified the evolution of the protein-coding genes.

Chloroplast genomes of Bulbophyllum Asian and South American clades were different
Comparative cp genome analyses have revealed that cp genomes are conserved in genome sizes, structures, and gene contents [26][27][28]. Because evolutionary rates of cp genomes are slower than nuclear and mitochondrial genomes [3,29], complete cp genomes are useful resources for phylogenetic analysis and species identification [30][31][32]. With the rapid development of cp genome researches, there have been comprehensive understandings about the cp genome characteristics. For example, (i) cp genome substitution rates are considerably lower in IR regions than in SC regions [3,11,12]; (ii) the repeat sequences played an important role in rearrangements of cp genomes [13][14][15]; (iii) mutational hotspots are genus specific [33,34]. However, the differences of the cp genomes in different continents have not been analyzed. The genus Bulbophyllum, which is widely distributed in Asia, south America and other places [17,18], is an excellent source for the comparison of cp genome features, cp genome junctions and mutational hotspots.
We compared the overall structures and variations of Bulbophyllum cp genomes. All results showed that there were considerable differences in overall cp genome features between AN and SA clades. Firstly, they have different cp genome features. For example, (i) the overall, LSC and SSC GC contents of AN clade are higher than SA clade; (ii) part of the rpl32 orientations in AN clade were different from SA clade, which caused by an inversion; (iii) except LSC LDRs and IR SSRs distribution densities, the LDRs and SSRs distribution densities in SA clade were higher than in AN clade. Secondly, J SB s between two clades varied significantly. AN and SA clades had different types of J SB s. There was no type B J SB s in AN clade and there were more type C J SB s in SA clade. Thirdly, the distributions and kinds of mutational hotspots between two clades were significantly different. Niu et al. (2017) found specific barcodes searched by 8-10 closely related cp genomes from specific genus can uncover their cp genome features [33]. Therefore, the mutational hotspots of two clades estimated in this study can reflect the variations of non-coding loci. However, there were only two hotspots shared between two clades, which indicated that the AN and SA clades had discordant evolution in noncoding regions. In conclusion, AN and SA clades had considerable differences in overall cp genome features.

The cp genome structures between Asian and South American clades were different under geographic isolation
Hybridization, a driver of plant evolution, is common among terrestrial orchids [35]. Although dust-like seeds have the capacity to travel long distance [36][37][38], the results of this study showed that Bulbophyllum AN clade has diverged completely from SA clade in the late Oligocene (21.50-30.12 mya) [18]. Because the results of the JML software have ruled out the possibility of hybridization between the two clades [39], Bulbophyllum AN and SA clades have evolved independently for at least 25.81 million years. Our subsequent analyses revealed significant cp genome structural variations between two clades.
The insertions and deletions (InDels) are important structural variations of cp genomes [32]. In order to evaluate the structural variations of the cp genomes during the evolution of Bulbophyllum, we calculated the total InDels lengths of each Bulbophyllum by the aligned complete cp genome sequences, with D. huoshanense as outgroup. There were 5,314 to 14,498 bp deletions and 4,216 to 10,652 bp insertions in Bulbophyllum. Obviously, the lengths of deletions were longer than insertions, which is consistent with previous studies [16,40]. To obtain more detailed information about InDels, we calculated the distribution densities of InDels in different cp genome regions. The distribution densities of insertions in LSC, IR, and SSC regions were 22.7-48.9 bp/kbp, 4.8-46.1 bp/kbp, and 29.4-286.9 bp/kbp, respectively. And the deletions distribution densities in LSC, IR and SSC regions were 37.8-130.5 bp/kbp, 16.2-92.3 bp/kbp, and 24-389.1 bp/kbp, respectively. The results revealed that the distributions of InDels are dependent on their locations in cp genomes [16,41,42], e.g., associated with low GC contents.
To estimate the pace of structural variations in the Bulbophyllum cp genomes, we dated the occurrence rates of InDels by located them at the BEAST tree branches. The results showed that, during the past ~ 10.96 million years since the late Eocene, the insertions and deletions occurred at the speeds of 67.15 bp/myr and 194.07 bp/myr. Then, AN clade and SA clade diverged at ~ 25.81 mya. Our results further revealed that InDels remarkably varied across different lineages [40]. Nevertheless, the most InDels occurrence rates of AN Bulbophyllum were higher than SA Bulbophyllum. We speculated that there were two main reasons for the higher occurrence rates of InDels in the AN clade: (1) the results of Gamisch et al. (2021) indicated that Asia was the original continent of the Bulbophyllum orchids [43]; (2) Of all the continents where Bulbophyllum orchids grow, Asia has the largest suitable area for speciation and niche expansion of the genus Bulbophyllum [43]. In conclusion, the cp genome structures between two clades were different under geographic isolation. And for further study, InDels may be an important indicator of species evolution.

Crassulacean acid metabolism (CAM) pathway may be the inducement of cp gene differentiation
Crassulacean acid metabolism (CAM) is the typical plant photosynthetic pathway that improves water use efficiency of plants [44]. About 10% of orchid species have been confirmed to be CAM plants [45][46][47], and 50% of Orchidaceae species were anticipated to be CAM plants [48]. CAM has evolved multiple independent times in the Orchidaceae [49]. Phylogenetic analyses of the neotropical orchids indicated that CAM has evolved independently at least 10 times [48]. For example, CAM in Dendrobium, the sister genus of Bulbophyllum, has arisen for at least eight times [49]. The Bulbophyllum orchids are typical CAM orchids. Although the C 3 pathway is the main photosynthetic pathway of Bulbophyllum presently, the CAM pathway plays an important role in adapting to new ecological niches and increasing species diversity [43].
In order to evaluate the effects of CAM pathway on cp gene evolution in the genus Bulbophyllum, Selective pressure analysis of functional genes has been employed [50][51][52]. Non-synonymous (dN), synonymous (dS) nucleotide substitution rates and nonsynonymous/synonymous rate ratio (ω = dN/dS) are widely used as indicators of adaptive evolution [40]. The values of dN and dS on all protein-coding genes between two clades were compared, and we found three photosynthesis genes, ten self-replication genes and three other genes, which have significantly different ω values. The three photosynthesis genes (psbZ, atpE and atpA) encode fractions of the photosystems and the thylakoid ATP synthase complex. In addition, positively selective genes (ω values > 1) through the Bulbophyllum evolution were screened. There were six, five and three positively selective cp genes in the Bulbophyllum branch, AN branch and SA branch, respectively. And these genes were mostly distributed in the LSC regions, which is consistent with previous studies [40]. Because there were many photosynthesis genes, which are components of Photosystem II, among two clades under different selective pressures, the CAM pathway may play an important role in adaptive evolution of Bulbophyllum. In addition, Hu et al. (2022) assessed the origin and loss of CAM in the Bulbophyllum since middle Miocene using two cp genes (matK and psbA) and two nuclear sequences (ITS and Xdh) [53]. They found that although CAM increased the adaptability of the Bulbophyllum plants to specific conditions, it was less competitive than C 3 in the long term. Predictably, the role of CAM in the species evolution of Bulbophyllum can be further explored using the complete cp genomes.
Before the ancestors of the Bulbophyllum diverged from Dendrobium at late Eocene, CAM and epiphytism in orchids are likely to have originated about 65 mya [54,55]. Then, some of the Bulbophyllum photosynthetic genes (psbB, psbF and rbcL) had evolved to adapt to the changeable environment and expand habitat region. At late Oligocene, AN clade diverged from other Bulbophyllum clade, through which SA clade had no gene flow with AN clade. The cp genomes of two clades evolved to different features under different environments. In this process, the CAM pathway affects the selective pressures of photosynthetic genes. Therefore, in subsequent studies, CAM studies and cp genome studies will be more closely linked to explore species evolution of Bulbophyllum.

Conclusions
In this study, the nine Bulbophyllum cp genomes were newly sequenced and assembled. Comparative analyses showed that there were considerable differences in overall cp genome features between AN and SA clades in three aspects, including basic cp genome features, JS B s and mutational hotspots. Then we found that the cp genome structures between two clades were different under geographic isolation by estimating the occurrence rates of the InDels. Finally, the results showed that long-term geographic isolation put AN and SA Bulbophyllum cp genes under different selective pressures. All results indicated that the overall structural characteristics of Bulbophyllum cp genomes diverged during the long-term geographic isolation, and the CAM pathway may play an important role in the cp genes evolution of Bulbophyllum.

Plant materials and DNA extraction
In this study, nine medicinal Bulbophyllum orchids sequenced (B.

DNA sequencing, assembly and annotation
The total genomic DNA of nine Bulbophyllum orchids was sequenced using Illumina Hiseq4000 platform (Illumina Inc, San Diego, CA, USA). Approximately 5.0 Gb of raw data were generated with 150 bp pairedend reads for each sample. The fragments with coverage < 50 × were deleted and filtered paired-end reads were assembled on CLC Genomics Workbench v8.5.1 (CLC Bio, Aarhus, Denmark), with reference Dendrobium huoshanense C. Z. Tang et S. J. Cheng. The four junctions between LSC/SSC and IRs were validated with PCR amplification. The assembled cp genomes were annotated using DOGMA v1.2 and tRNAscan-SE v1.21 [56,57]. The boundaries of annotated genes were confirmed by multiple sequence alignment.

Comparative analysis of cp genomes
The gene location information was extracted, and the IR/ SC junction information was collated with the gene location information. The GC contents of 27 Bulbophyllum orchids were analyzed. The nine newly sequenced Bulbophyllum cp genomes were compared using online mVISTA (https:// genome. lbl. gov/ vista/ mvista/ submit. shtml) on LAGAN model, with reference D. huoshanense [58].

Characterization of repeat sequences and simple sequence repeats
The REPuter program (https:// bibis erv. cebit ec. uni-biele feld. de/ reput er) was used to identify the four different types of repeats (forward, reverse, complement and palindromic repeats), with sequence identity ≥ 90%, minimum repeat size ≥ 30 bp, and Hamming distance = 3 [59]. Simple sequence repeats (SSRs) were discovered using the online program MISA (https:// webbl ast. ipkgater sleben. de/ misa/) with the following parameters: 8 for mononucleotide motifs, 5 for polynucleotide motifs [60]. Then the distribution densities of repeat sequences and SSRs on LSC, SSC and IR regions were compared.

IR/SC junctions map
Refer to the method of Zhu et al. (2018) [42], the IR/SC junctions map of 19 AN Bulbophyllum orchids, eight SA Bulbophyllum orchids and D. huoshanense was drawn.

Mutational hotspots
Based on 19 AN Bulbophyllum cp genomes, the top ten hotspots in AN clade were screened. Based on eight SA Bulbophyllum cp genomes, the top ten mutational hotspots in SA clade were screened. The gene location information was transformed into the non-coding region location information, and the sequence of each non-coding region was extracted (ycf1-rpl32 was taken as a whole fragment due to the loss of ndhF). Each noncoding region was aligned with MEGA 5.0 [61], and gaps at both ends were deleted. SNPs, InDels, and conserved sites were calculated by DnaSP v5 [62]. Non-coding regions, of which conserved sites were less than 100 bp, were removed. Sequence variabilities were calculated as follows: Sequence Variabilities = (SNPs + InDels) / (SNPs + InDels + Conserved sites) × 100% [34,63].

Hybridization testing
The cp genomes and ITS sequences of 17 Bulbophyllum orchids, two D. huoshanense, four D. moniliforme and five D. officinale were aligned using MAFFT 7.220 [64], and were connected together. Under the rule of AIC (Akaike information criterion), the optimum base substitution model calculated by Modeltest 3.7 was GTR + I + Γ [65]. The species tree was constructed using BEAST2 [66]. The Markov Chain Monte Carlo (MCMC) chains were performed to check convergence with 10,000,000 generations. The probability of hybridization was calculated using JML [67]. The significance level was 0.01.

Phylogenetic analysis
Phylogenetic relationships were analyzed based on 61 complete cp genomes, including one dicotyledonous plant, eight monocotyledonous non-orchids, and 52 orchids (Table S1). The cp genome sequences were aligned using MAFFT 7.220 [64]. The conserved loci were selected by Gblocks v.0.91b with the following parameters: minimum number of sequences for a conserved position: 37, minimum number of sequences for a flank position: 62, maximum number of contiguous nonconserved positions: 8, minimum length of a block: 10, allowed gap positions: none [68]. Under the rule of AIC (Akaike information criterion), the optimum base substitution model calculated by Modeltest 3.7 was GTR + I + Γ [65]. The Maximum Likelihood (ML) phylogenetic tree was constructed using RAxML (version 7.4.2) with 1000 rapid bootstrap inferences [69]. The outgroup was Arabidopsis thaliana. The BI analysis was made by using MrBayes 3.2.7 with 1000,000 generations [70]. Trees were sampled every 1,000 generations, and the first 25% of these were discarded. The remaining trees were used to build the Bayesian tree of posterior probabilities. In addition, ITS, psbA, matK, rbcL and cp genomes of 27 orchids were used to reconstructed ML trees with 1000 rapid bootstrap inferences.
(2) The stem age of Lemnoideae was set as 62 Mya (prior distribution: normal, mean: 62, sd: 3) [74]. (3) Based on the fossil record of Dendrobium, the Crown age of Dendrobium (the divergence time between the Dendrobium Asian clade and the Australian clade) was set at 21 Mya (prior distribution: normal, mean: 21, sd: 5) [25,75]. Three independent MCMC were performed to check convergence, each with 10,000,000 generations. LogCombiner was used to integrate the data results of three independent runs and remove the top 10% of unstable data.

Structural variation analysis of Bulbophyllum cp genomes
The cp genome sequences of 27 Bulbophyllum orchids and D. huoshanense were aligned using MAFFT 7.220 [64]. The InDels of each Bulbophyllum cp genome were counted, with D. huoshanense as reference. Then, the common InDels of 27 Bulbophyllum cp genomes were counted to calculate the InDels occurrence rates of AN, SA and Bulbophyllum branches. The above common InDels were excluded to calculate the recent occurrence rates of InDels in each Bulbophyllum cp genome.

Nucleotide substitutions rates and positive selection analysis of protein-coding genes
The molecular evolution of 63 cp protein-coding genes were investigated from 27 Bulbophyllum orchids and D. huoshanense. The values of dN, dS and ω were estimated by the codonML in the PAML software (version 4.4) with reference D. huoshanense [76,77]. Chloroplast proteincoding genes, whose ω values were different between two clades (T-test for Independent Samples) significantly, were screened. EasyCodeML was used to detect positively selective genes in the Bulbophyllum branch, AN branch and SA branch under Branch model with 5% significance level, respectively [40].